# Fit Hidden Markov Models using Template Model Builder

## Documentation for package ‘hmmTMB’ version 1.1.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

as_character_formula | Read formula with as.character without splitting
as_sparse | Transforms matrix to dgTMatrix
bdiag_check | Create block diagonal matrix (safe version)
check_contiguous | Check values in vector are contiguous
cov_grid | Grid of covariates
Dist | R6 class for probability distribution
dvm | Density function of von Mises distribution
dwrpcauchy | Density function of wrapped Cauchy distribution
find_re | Find s(, bs = "re") terms in formula
gdeterminant | Generalized matrix determinant
HMM | R6 class for hidden Markov model
hmmTMB_cols | hmmTMB colour palette
invmlogit | Multivarite inverse logit function
is_whole_number | Check if number of whole number
logLik.HMM | logLik function for SDE objects
logsumexp | Log of sum of exponentials
make_cov | Make covariance matrix from standard deviations and correlations
make_formulas | Process formulas and store in nested list
make_matrices | Create model matrices
MarkovChain | R6 class for HMM hidden process model
mlogit | Multivariate logit function
mvnorm_invlink | Multivariate Normal inverse link function
mvnorm_link | Multivariate Normal link function
na_fill | Fill in NAs
Observation | R6 class for HMM observation model
prec_to_cov | Get covariance matrix from precision matrix
quad_pos_solve | Solve for positive root of quadratic ax^2 + bx + c = 0 when it exists
rvm | Sample from von Mises distribution
rwrpcauchy | Sample from wrapped Cauchy distribution
strip_comments | Strip comments marked with a hash from a character vector
update.HMM | Update a model to a new model by changing one formula